From CJMungall at lbl.gov Wed Feb 2 09:50:23 2011
From: CJMungall at lbl.gov (Chris Mungall)
Date: Wed, 2 Feb 2011 09:50:23 -0800
Subject: [Ontology-editors] TermGenie back up
Message-ID: <37B4F410-605D-4464-B64A-B3647A052373@lbl.gov>
there will be occasional stalls until SF CVS service is returned (even though GO uses its own CVS, TG has a dependency on a file in sf cvs). Ping me if it happens again
From aji at ebi.ac.uk Mon Feb 7 10:44:16 2011
From: aji at ebi.ac.uk (Amelia Ireland)
Date: Mon, 7 Feb 2011 10:44:16 -0800
Subject: [Ontology-editors] [pamgo-discussion] Re: Fwd: New terms for
'behavioral interaction between organisms'
In-Reply-To:
References: <4D502167.9040601@ebi.ac.uk>
Message-ID: <38EC4102-1539-4DA4-8B2A-2CB435F06A20@ebi.ac.uk>
[ cc-ing the ontology editors to get their opinion ]
On 7 Feb 2011, at 09:44, Brett Tyler wrote:
> I don't think that 'suckling behavior ; GO:0001967' should be given
> the parent 'feeding on other organism ; GO:NEW'? because the
> definition and intent refer to consuming part or all of the
> organism, rather than consuming an acellular secretion from the
> organism. If suckling behavior were included here, then for instance
> coprophagy should also be included.
Perhaps there needs to be a more generic 'feeding from other organism'
term that encompasses "intentional" feeding mechanisms such as
suckling and other behaviours such as parent birds regurgitating food,
as well as "unintentional" feeding (n.b. the terms should not mention
volition or intention of feeding). Currently "feeding on other
organism" is defined as
"The behaviour of consuming the whole or part of another organism for
the purposes of nutrition."
so the more generic term could be
The behaviour of consuming material from another organism for the
purposes of nutrition; this material may be a corporeal part of the
organism or a secretion produced by the organism.
I don't know if there are cases of overlap, i.e. where the second
organism consumes secretions from the first and then starts to consume
the organism itself. It sounds familiar from various wildlife
programmes, though...
As for coprophagy, dogs will indulge in coprophagy of their own
secretions; if it were to be added, it would need both self- and non-
self terms.
> At 4:44 PM +0000 2/7/11, Emily Dimmer wrote:
>> Dear PAMGO folk,
>>
>> Coming back to some 'behavioral interaction between organisms' GO
>> terms,
>> please could you take a look at the proposed terms in the following
>> SourceForge entry:
>> https://sourceforge.net/tracker/?func=detail&aid=3124476&group_id=36855&atid=440764
>>
>> One question is whether 'suckling behavior ; GO:0001967' should be
>> given
>> the parent 'feeding on other organism ; GO:NEW'?
>>
>> If there are no objections/modifications to the proposed terms, I can
>> add them in to GO this week.
>>
>> Many thanks,
>> Rebecca
>>
>> --
>> Dr Rebecca Foulger
>> GO Editorial Office
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridgeshire, UK
>> CB10 1SD
>>
>> p: +44 1223 492523
>> f: +44 1223 494468
>>
>> *******************************************************************************
>> Virginia Bioinformatics Institute PAMGO Discussion Mailing List
>> *******************************************************************************
>
> --
> *****************
> Brett Tyler
> Professor
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Washington Street
> Blacksburg, VA 24061-0477
>
> Telephone: (540) 231-7318
> Fax: (540) 231-2606
> Email: bmtyler at vt.edu
> Web: https://www.vbi.vt.edu/article/articleview/141
> Twitter: @BrettTylerVT
>
> Administrative Assistant:
> Maureen Lawrence-Kuether
> Telephone: (540) 231-5995
> Email: mlawre04 at vbi.vt.edu
> *****************
> *******************************************************************************
> Virginia Bioinformatics Institute PAMGO Discussion Mailing List
> *******************************************************************************
--
Amelia Ireland
GO Editorial Office
http://www.berkeleybop.org || http://www.ebi.ac.uk
Preventing Euthanasia Through Rescue: http://petrescueinc.org
From rfoulger at ebi.ac.uk Tue Feb 8 02:52:09 2011
From: rfoulger at ebi.ac.uk (Rebecca Foulger)
Date: Tue, 08 Feb 2011 10:52:09 +0000
Subject: [Ontology-editors] [pamgo-discussion] Re: Fwd: New terms for
'behavioral interaction between organisms'
In-Reply-To: <38EC4102-1539-4DA4-8B2A-2CB435F06A20@ebi.ac.uk>
References: <4D502167.9040601@ebi.ac.uk>
<38EC4102-1539-4DA4-8B2A-2CB435F06A20@ebi.ac.uk>
Message-ID: <4D512059.8060206@ebi.ac.uk>
Thanks Brett and Amelia.
Would the existing proposed 'feeding on tissue' term be enough to
distinguish an organism consuming another organism/part of another
organism, from the 'intentional' suckling behavior, if we want a generic
term?:
behavioral interaction between organisms ; GO:0051705
--[i] feeding from other organism (generic term)
----[i] suckling behavior ; GO:0001967
----[i] feeding on tissue of other organism (broad synonym: feeding on
other organism?)
feeding from other organism (generic term)
synonym: deriving nutrients from other organism
The behavior of consuming material from another organism for the
purposes of nutrition; this material may be a corporeal part of the
organism or a secretion produced by the organism.
GOC:ai
The existing terms are to annotate the proteome of organisms who are
receiving the nutrients. For parent birds regurgitating their food, the
behavior is occurring in the adult (the giver of nutrition), so it
wouldn't currently fit.
On a second question:
Is there a difference between:
predation ; GO:NEW
The behavior by which a predator (an animal that is hunting) hunts and
then feeds on its prey (the animal that is attacked). This term is not
intended to encompass herbivore grazing or parasitic interactions.
and
predatory aggressive behavior ; GO:0002120
Aggressive behavior involving attack on prey by a predator,
characterized by lack of threatening displays, silence, and no sex
differences.
(definition needs fixing).
I'll update the SF entry,
thanks,
Becky
ps:please could someone forward to the pamgo list... or subscribe me to
the pamgo list (I can't post to the list)- thanks!
On 07/02/2011 18:44, Amelia Ireland wrote:
> [ cc-ing the ontology editors to get their opinion ]
>
> On 7 Feb 2011, at 09:44, Brett Tyler wrote:
>
>> I don't think that 'suckling behavior ; GO:0001967' should be given
>> the parent 'feeding on other organism ; GO:NEW'? because the
>> definition and intent refer to consuming part or all of the organism,
>> rather than consuming an acellular secretion from the organism. If
>> suckling behavior were included here, then for instance coprophagy
>> should also be included.
>
> Perhaps there needs to be a more generic 'feeding from other organism'
> term that encompasses "intentional" feeding mechanisms such as
> suckling and other behaviours such as parent birds regurgitating food,
> as well as "unintentional" feeding (n.b. the terms should not mention
> volition or intention of feeding). Currently "feeding on other
> organism" is defined as
>
> "The behaviour of consuming the whole or part of another organism for
> the purposes of nutrition."
>
> so the more generic term could be
>
> The behaviour of consuming material from another organism for the
> purposes of nutrition; this material may be a corporeal part of the
> organism or a secretion produced by the organism.
>
> I don't know if there are cases of overlap, i.e. where the second
> organism consumes secretions from the first and then starts to consume
> the organism itself. It sounds familiar from various wildlife
> programmes, though...
>
> As for coprophagy, dogs will indulge in coprophagy of their own
> secretions; if it were to be added, it would need both self- and
> non-self terms.
>
>
>
>> At 4:44 PM +0000 2/7/11, Emily Dimmer wrote:
>>> Dear PAMGO folk,
>>>
>>> Coming back to some 'behavioral interaction between organisms' GO
>>> terms,
>>> please could you take a look at the proposed terms in the following
>>> SourceForge entry:
>>> https://sourceforge.net/tracker/?func=detail&aid=3124476&group_id=36855&atid=440764
>>>
>>>
>>> One question is whether 'suckling behavior ; GO:0001967' should be
>>> given
>>> the parent 'feeding on other organism ; GO:NEW'?
>>>
>>> If there are no objections/modifications to the proposed terms, I can
>>> add them in to GO this week.
>>>
>>> Many thanks,
>>> Rebecca
>>>
>>> --
>>> Dr Rebecca Foulger
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492523
>>> f: +44 1223 494468
>>>
>>> *******************************************************************************
>>>
>>> Virginia Bioinformatics Institute PAMGO Discussion Mailing List
>>> *******************************************************************************
>>>
>>
>> --
>> *****************
>> Brett Tyler
>> Professor
>> Virginia Bioinformatics Institute
>> Virginia Polytechnic Institute and State University
>> Washington Street
>> Blacksburg, VA 24061-0477
>>
>> Telephone: (540) 231-7318
>> Fax: (540) 231-2606
>> Email: bmtyler at vt.edu
>> Web: https://www.vbi.vt.edu/article/articleview/141
>> Twitter: @BrettTylerVT
>>
>> Administrative Assistant:
>> Maureen Lawrence-Kuether
>> Telephone: (540) 231-5995
>> Email: mlawre04 at vbi.vt.edu
>> *****************
>> *******************************************************************************
>>
>> Virginia Bioinformatics Institute PAMGO Discussion Mailing List
>> *******************************************************************************
>>
>
> --
> Amelia Ireland
> GO Editorial Office
> http://www.berkeleybop.org || http://www.ebi.ac.uk
> Preventing Euthanasia Through Rescue: http://petrescueinc.org
>
>
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
--
Dr Rebecca Foulger
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492523
f: +44 1223 494468
From huntley at ebi.ac.uk Tue Feb 8 03:52:59 2011
From: huntley at ebi.ac.uk (Rachael Huntley)
Date: Tue, 08 Feb 2011 11:52:59 +0000
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To:
References: <4D4BD21C.4070003@ebi.ac.uk>
Message-ID: <4D512E9B.2060208@ebi.ac.uk>
Hi Heather,
I am going to have to refer you to the ontology editors for these
questions as they will undoubtedly give much better answers than I can.
All: Heather would like to analyse a dataset but would like to know
which relationships to include and which are considered parent-child.
What are the implications of including/not including 'regulates'
relationships in the analysis, especially for Function?
Can you distinguish regulates terms that regulate processes from those
that regulate function?
Full story below.
Thanks for your help.
Rachael.
On 07/02/2011 20:02, Heather Wick wrote:
> Hi Rachael,
>
> Thanks for the clarification on has_part, that helps a lot.
>
> Your point about regulation terms is something we had not yet
> considered and I'm glad you brought it up. I was under the impression
> that the process, function, and component ontologies were separate and
> that there were no relationships between them; so that all "regulation
> of" terms were biological process terms and had biological process
> parentage, even if they regulated an activity. But I see now that the
> "regulates" relationship can bridge the ontologies (thanks in part to
> the new color coded Graph View display in AmiGO). Is there any way to
> distinguish whether a term regulates something in its own ontology vs.
> a different ontology if we did want to keep the biological process
> regulation terms but not molecular function regulation terms? I've
> been trying to understand how we could determine that based on the
> information in this file, since this is the file we are writing our
> program around:
> http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
>
> Another point of confusion is that I can't find any explanations on
> what the terms "relationship:" and "intersection_of:" mean in this
> file, even in the informational sections on relationships
> (http://www.obofoundry.org/ro/,
> http://www.geneontology.org/GO.ontology.relations.shtml). Do they
> indicate a parent-child relationship? For that matter, are there any
> other terms besides "is_a" and "part_of" that describe "true"
> parent-child relationships?
> Just so I understand you correctly, are you saying that GO does not
> consider a term like "regulation of angiogenesis" to be a child of
> "angiogenesis?" I thought that these kinds of terms were considered to
> have a parent-child relationship and that the genes annotated to
> "regulation of angiogenesis" would also be annotated to "angiogenesis"
> and up through the tree automatically by GO. For what relationships
> does GO carry the annotation up?
>
> Thank you for all of your help!
> ~ Heather
>
> On Fri, Feb 4, 2011 at 5:17 AM, Rachael Huntley > wrote:
>
> Hi Heather,
>
> Yes, the has_part relationship is getting many people confused! It
> is not a true parent-child relationship so I think you can ignore
> it for your purposes.
>
> It is kind of a reverse relationship, so if you look at
> http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004055#term=ancchart you
> see that 'urea cycle' has_part 'arginosuccinate synthase activity'
> (the arrow between the terms is going in the opposite direction),
> which means the urea cycle always involves arginosuccinate
> synthase activity, but if a protein has arginosuccinate synthase
> activity it is not necessarily taking part in the urea cycle.
>
> On top of this, we are aware that QuickGO has some display issues
> with the has_part relationships, which are misleading. So in the
> example of protein phosphatase 2A binding
> (http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051721#term=ancchart)
> it looks like protein phosphatase 2A binding is related all the
> way up the chart to transcription, which is not true. So we need
> to sort out this display so it accurately represents the
> relationships and their traversal.
>
> You would need to think about whether you want to include the
> regulates relationships as well, because if a protein regulates a
> process, it is not necessarily directly involved in that process.
> You probably wouldn't want to include regulates relations for
> function terms as a protein that regulates a function probably
> would not have that function itself, e.g. if it regulates a
> kinase, it may not be a kinase itself.
>
> In QuickGO you can choose which relations you want to include in a
> GO slim in the Filter -> GO Identifier menu (if you want further
> help on this just let me know).
>
> I hope this explains it a little better? I am not brilliant with
> has_part so if you have more questions, I could direct them to one
> of the ontology editors who should know more than me!
>
> Best wishes,
> Rachael.
>
>
> On 03/02/2011 17:06, Heather Wick wrote:
>> Hi Rachael,
>> DFLAT is currently working on a gene set collection similar to
>> what the Broad did in 2008 with its C5 collection, and as part of
>> that we're trying to sort through all the parent-child
>> relationships in GO to map gene sets of child terms to their
>> parents. As far as I can tell, "is_a," "part_of," and "regulates"
>> (including negatively_ and positively) describe parent-child
>> relationships, but I'm a bit confused about the term "has_part."
>> On this page
>> http://www.geneontology.org/GO.ontology-ext.relations.shtml#haspart
>> it says "A /necessarily has part/ B. If A exists, B will always
>> exist; however, if B exists, we cannot say for certain that A
>> exists." This suggests that if A has_part B, then B is a parent
>> of A. Is that correct? Or is "has_part" not really considered to
>> describe a parent-child relationship? For example, I noticed that
>> "Urea cycle" has_part "argininosuccinate synthase activity," but
>> "argininosuccinate synthase activity" is listed as not having any
>> children.
>>
>> Aside from "is_a," "part_of,", and "regulates," are there any
>> other terms that describe a parent-child relationship?
>> Thanks,
>> ~ Heather
>>
>> --
>> Heather Wick
>> Research Coordinator
>> Tufts University Computer Science Department
>> hwick at cs.tufts.edu
>
>
> --
> GOA and IntAct Curator
> European Bioinformatics Institute
> Welcome Trust Genome Campus
> Hinxton
> Cambridge, CB10 1SD
> UK
>
> Tel: 01223 492515
> Fax: 01223 494468
> Email:huntley at ebi.ac.uk
> GOA:http://www.ebi.ac.uk/GOA
> IntAct:http://www.ebi.ac.uk/intact
>
>
>
>
> --
> Heather Wick
> Research Coordinator
> Tufts University Computer Science Department
> hwick at cs.tufts.edu
--
GOA and IntAct Curator
European Bioinformatics Institute
Welcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
UK
Tel: 01223 492515
Fax: 01223 494468
Email: huntley at ebi.ac.uk
GOA: http://www.ebi.ac.uk/GOA
IntAct: http://www.ebi.ac.uk/intact
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From huntley at ebi.ac.uk Wed Feb 9 07:33:22 2011
From: huntley at ebi.ac.uk (Rachael Huntley)
Date: Wed, 09 Feb 2011 15:33:22 +0000
Subject: [Ontology-editors] Problem with gene_ontology_ext.obo
In-Reply-To:
References:
Message-ID: <4D52B3C2.3010709@ebi.ac.uk>
Hi,
Could someone please take a look at this?
Thanks,
Rachael.
>
> Subject:
> GO Help query (from website)
> From:
> olivier.langella at moulon.inra.fr
> Date:
> Wed, 9 Feb 2011 01:45:27 -0800
>
> To:
> gohelp at genome.stanford.edu
>
>
> Email:olivier.langella at moulon.inra.fr
> Name: General query (from Langella)
> Text: Hello,
>
> I've tried to download the latest daily build of Gene Ontology OBO file : "gene_ontology_ext.obo".
> I've some difficulty trying to use in my own database.
> the term id: GO:0004152 in this file contains two odd lines :
> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT systematic_synonym [EC:1.3.5.2]
> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT [EC:1.3.5.2]
> the two lines are very similar and refers to the same synonym : it leads my OBO file parser to a crash...
> is this a bug in this daily build file or a feature of the OBO file format ?
> There is a similar problem with :
> id: GO:0021513
> synonym: "spinal cord dorsal-ventral patterning" EXACT [GOC:mah]
> synonym: "spinal cord dorsal-ventral patterning" EXACT []
>
> Thank you,
> Olivier
--
GOA and IntAct Curator
European Bioinformatics Institute
Welcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
UK
Tel: 01223 492515
Fax: 01223 494468
Email: huntley at ebi.ac.uk
GOA: http://www.ebi.ac.uk/GOA
IntAct: http://www.ebi.ac.uk/intact
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From midori.harris at gmail.com Wed Feb 9 07:39:26 2011
From: midori.harris at gmail.com (Midori Harris)
Date: Wed, 9 Feb 2011 15:39:26 +0000
Subject: [Ontology-editors] Problem with gene_ontology_ext.obo
In-Reply-To: <4D52B3C2.3010709@ebi.ac.uk>
References:
<4D52B3C2.3010709@ebi.ac.uk>
Message-ID:
I'm happy to delete the offending duplicates. But it would be nice to have a better way to detect them than having a user report a crash ...
m
On 9 Feb 2011, at 3:33 pm, Rachael Huntley wrote:
> Hi,
>
> Could someone please take a look at this?
>
> Thanks,
> Rachael.
>>
>>
>> Subject: GO Help query (from website)
>> From: olivier.langella at moulon.inra.fr
>> Date: Wed, 9 Feb 2011 01:45:27 -0800
>> To: gohelp at genome.stanford.edu
>> Email: olivier.langella at moulon.inra.fr
>>
>> Name: General query (from Langella)
>> Text: Hello,
>>
>> I've tried to download the latest daily build of Gene Ontology OBO file : "gene_ontology_ext.obo".
>> I've some difficulty trying to use in my own database.
>> the term id: GO:0004152 in this file contains two odd lines :
>> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT systematic_synonym [EC:1.3.5.2]
>> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT [EC:1.3.5.2]
>> the two lines are very similar and refers to the same synonym : it leads my OBO file parser to a crash...
>> is this a bug in this daily build file or a feature of the OBO file format ?
>> There is a similar problem with :
>> id: GO:0021513
>> synonym: "spinal cord dorsal-ventral patterning" EXACT [GOC:mah]
>> synonym: "spinal cord dorsal-ventral patterning" EXACT []
>>
>> Thank you,
>> Olivier
>>
>
>
> --
> GOA and IntAct Curator
> European Bioinformatics Institute
> Welcome Trust Genome Campus
> Hinxton
> Cambridge, CB10 1SD
> UK
>
> Tel: 01223 492515
> Fax: 01223 494468
> Email:
> huntley at ebi.ac.uk
>
> GOA:
> http://www.ebi.ac.uk/GOA
>
> IntAct:
> http://www.ebi.ac.uk/intact
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
From cjmungall at lbl.gov Wed Feb 9 08:40:00 2011
From: cjmungall at lbl.gov (Chris Mungall)
Date: Wed, 9 Feb 2011 11:40:00 -0500
Subject: [Ontology-editors] Problem with gene_ontology_ext.obo
In-Reply-To:
References:
<4D52B3C2.3010709@ebi.ac.uk>
Message-ID: <4954EA54-79B5-448C-83CF-88A1767E24FD@lbl.gov>
There's nothing in the spec that says a parser should crash. It's syntactically valid, but not good practice - can you add an OE request for a verification check?
On Feb 9, 2011, at 10:39 AM, Midori Harris wrote:
> I'm happy to delete the offending duplicates. But it would be nice to have a better way to detect them than having a user report a crash ...
>
> m
>
> On 9 Feb 2011, at 3:33 pm, Rachael Huntley wrote:
>
>> Hi,
>>
>> Could someone please take a look at this?
>>
>> Thanks,
>> Rachael.
>>>
>>>
>>> Subject: GO Help query (from website)
>>> From: olivier.langella at moulon.inra.fr
>>> Date: Wed, 9 Feb 2011 01:45:27 -0800
>>> To: gohelp at genome.stanford.edu
>>> Email: olivier.langella at moulon.inra.fr
>>>
>>> Name: General query (from Langella)
>>> Text: Hello,
>>>
>>> I've tried to download the latest daily build of Gene Ontology OBO file : "gene_ontology_ext.obo".
>>> I've some difficulty trying to use in my own database.
>>> the term id: GO:0004152 in this file contains two odd lines :
>>> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT systematic_synonym [EC:1.3.5.2]
>>> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT [EC:1.3.5.2]
>>> the two lines are very similar and refers to the same synonym : it leads my OBO file parser to a crash...
>>> is this a bug in this daily build file or a feature of the OBO file format ?
>>> There is a similar problem with :
>>> id: GO:0021513
>>> synonym: "spinal cord dorsal-ventral patterning" EXACT [GOC:mah]
>>> synonym: "spinal cord dorsal-ventral patterning" EXACT []
>>>
>>> Thank you,
>>> Olivier
>>>
>>
>>
>> --
>> GOA and IntAct Curator
>> European Bioinformatics Institute
>> Welcome Trust Genome Campus
>> Hinxton
>> Cambridge, CB10 1SD
>> UK
>>
>> Tel: 01223 492515
>> Fax: 01223 494468
>> Email:
>> huntley at ebi.ac.uk
>>
>> GOA:
>> http://www.ebi.ac.uk/GOA
>>
>> IntAct:
>> http://www.ebi.ac.uk/intact
>> _______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
From midori.harris at gmail.com Wed Feb 9 08:53:38 2011
From: midori.harris at gmail.com (Midori Harris)
Date: Wed, 9 Feb 2011 16:53:38 +0000
Subject: [Ontology-editors] Problem with gene_ontology_ext.obo
In-Reply-To: <4954EA54-79B5-448C-83CF-88A1767E24FD@lbl.gov>
References:
<4D52B3C2.3010709@ebi.ac.uk>
<4954EA54-79B5-448C-83CF-88A1767E24FD@lbl.gov>
Message-ID:
ok:
https://sourceforge.net/tracker/?func=detail&aid=3176609&group_id=36855&atid=418260
On 9 Feb 2011, at 4:40 pm, Chris Mungall wrote:
>
> There's nothing in the spec that says a parser should crash. It's syntactically valid, but not good practice - can you add an OE request for a verification check?
>
> On Feb 9, 2011, at 10:39 AM, Midori Harris wrote:
>
>> I'm happy to delete the offending duplicates. But it would be nice to have a better way to detect them than having a user report a crash ...
>>
>> m
>>
>> On 9 Feb 2011, at 3:33 pm, Rachael Huntley wrote:
>>
>>> Hi,
>>>
>>> Could someone please take a look at this?
>>>
>>> Thanks,
>>> Rachael.
>>>>
>>>>
>>>> Subject: GO Help query (from website)
>>>> From: olivier.langella at moulon.inra.fr
>>>> Date: Wed, 9 Feb 2011 01:45:27 -0800
>>>> To: gohelp at genome.stanford.edu
>>>> Email: olivier.langella at moulon.inra.fr
>>>>
>>>> Name: General query (from Langella)
>>>> Text: Hello,
>>>>
>>>> I've tried to download the latest daily build of Gene Ontology OBO file : "gene_ontology_ext.obo".
>>>> I've some difficulty trying to use in my own database.
>>>> the term id: GO:0004152 in this file contains two odd lines :
>>>> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT systematic_synonym [EC:1.3.5.2]
>>>> synonym: "(S)-dihydroorotate:quinone oxidoreductase activity" EXACT [EC:1.3.5.2]
>>>> the two lines are very similar and refers to the same synonym : it leads my OBO file parser to a crash...
>>>> is this a bug in this daily build file or a feature of the OBO file format ?
>>>> There is a similar problem with :
>>>> id: GO:0021513
>>>> synonym: "spinal cord dorsal-ventral patterning" EXACT [GOC:mah]
>>>> synonym: "spinal cord dorsal-ventral patterning" EXACT []
>>>>
>>>> Thank you,
>>>> Olivier
>>>>
>>>
>>>
>>> --
>>> GOA and IntAct Curator
>>> European Bioinformatics Institute
>>> Welcome Trust Genome Campus
>>> Hinxton
>>> Cambridge, CB10 1SD
>>> UK
>>>
>>> Tel: 01223 492515
>>> Fax: 01223 494468
>>> Email:
>>> huntley at ebi.ac.uk
>>>
>>> GOA:
>>> http://www.ebi.ac.uk/GOA
>>>
>>> IntAct:
>>> http://www.ebi.ac.uk/intact
>>> _______________________________________________
>>> Ontology-editors mailing list
>>> Ontology-editors at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>>
>>
>> _______________________________________________
>> Ontology-editors mailing list
>> Ontology-editors at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
>
From rfoulger at ebi.ac.uk Thu Feb 10 06:25:19 2011
From: rfoulger at ebi.ac.uk (Rebecca Foulger)
Date: Thu, 10 Feb 2011 14:25:19 +0000
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To: <4D512E9B.2060208@ebi.ac.uk>
References: <4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk>
Message-ID: <4D53F54F.1080701@ebi.ac.uk>
Dear Heather,
You probably don't want to follow has_part relationships for a slim,
because they point from less specific to more specific (i.e. the
opposite way to 'is_a' and 'part_of' relationships).
For 'regulates' relationships, you should bear in mind that the parent
is not necessarily more general than the child (unlike is_a and
part_of). Like you say, you may want to include 'regulation of x
process' but not 'regulation of y function' in your slims. For example,
if you want to find kinases in your GOslim, you will not want to include
gene products that regulate kinases but do not necessarily have kinase
activity themselves. Whereas, if you want to find gene products involved
in the cell cycle, it may also be useful to include gene products that
regulate the cell cycle. There is extended documentation on the
relations and reasoning on them at
http://www.geneontology.org/GO.ontology-ext.relations.shtml.
Since all 'regulation of x process' and 'regulation of y function' terms
are process terms themselves, I do not know of a simple list separating
the two types. Have you used the OBO-Edit tool before (listed at
http://www.geneontology.org/GO.tools.shtml)? If so, you can download
OBO-Edit, load the .obo file into OBO-Edit and do a search for GO terms
that have 'regulation' in the term name, and have a molecular function
parent to generate a list. You can also perform more complex queries on
GO at: http://www.berkeleybop.org/goose.
One of the developers may be able to help you write a more specific query.
I hope that is of some help.
With best wishes,
Rebecca
On 08/02/2011 11:52, Rachael Huntley wrote:
> Hi Heather,
>
> I am going to have to refer you to the ontology editors for these
> questions as they will undoubtedly give much better answers than I can.
>
> All: Heather would like to analyse a dataset but would like to know
> which relationships to include and which are considered parent-child.
> What are the implications of including/not including 'regulates'
> relationships in the analysis, especially for Function?
> Can you distinguish regulates terms that regulate processes from those
> that regulate function?
> Full story below.
>
> Thanks for your help.
>
> Rachael.
>
> On 07/02/2011 20:02, Heather Wick wrote:
>> Hi Rachael,
>>
>> Thanks for the clarification on has_part, that helps a lot.
>>
>> Your point about regulation terms is something we had not yet
>> considered and I'm glad you brought it up. I was under the impression
>> that the process, function, and component ontologies were separate
>> and that there were no relationships between them; so that all
>> "regulation of" terms were biological process terms and had
>> biological process parentage, even if they regulated an activity. But
>> I see now that the "regulates" relationship can bridge the ontologies
>> (thanks in part to the new color coded Graph View display in AmiGO).
>> Is there any way to distinguish whether a term regulates something in
>> its own ontology vs. a different ontology if we did want to keep the
>> biological process regulation terms but not molecular function
>> regulation terms? I've been trying to understand how we could
>> determine that based on the information in this file, since this is
>> the file we are writing our program around:
>> http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
>>
>> Another point of confusion is that I can't find any explanations on
>> what the terms "relationship:" and "intersection_of:" mean in this
>> file, even in the informational sections on relationships
>> (http://www.obofoundry.org/ro/,
>> http://www.geneontology.org/GO.ontology.relations.shtml). Do they
>> indicate a parent-child relationship? For that matter, are there any
>> other terms besides "is_a" and "part_of" that describe "true"
>> parent-child relationships?
>> Just so I understand you correctly, are you saying that GO does not
>> consider a term like "regulation of angiogenesis" to be a child of
>> "angiogenesis?" I thought that these kinds of terms were considered
>> to have a parent-child relationship and that the genes annotated to
>> "regulation of angiogenesis" would also be annotated to
>> "angiogenesis" and up through the tree automatically by GO. For what
>> relationships does GO carry the annotation up?
>>
>> Thank you for all of your help!
>> ~ Heather
>>
>> On Fri, Feb 4, 2011 at 5:17 AM, Rachael Huntley > > wrote:
>>
>> Hi Heather,
>>
>> Yes, the has_part relationship is getting many people confused!
>> It is not a true parent-child relationship so I think you can
>> ignore it for your purposes.
>>
>> It is kind of a reverse relationship, so if you look at
>> http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004055#term=ancchart
>> you see that 'urea cycle' has_part 'arginosuccinate synthase
>> activity' (the arrow between the terms is going in the opposite
>> direction), which means the urea cycle always involves
>> arginosuccinate synthase activity, but if a protein has
>> arginosuccinate synthase activity it is not necessarily taking
>> part in the urea cycle.
>>
>> On top of this, we are aware that QuickGO has some display issues
>> with the has_part relationships, which are misleading. So in the
>> example of protein phosphatase 2A binding
>> (http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051721#term=ancchart)
>> it looks like protein phosphatase 2A binding is related all the
>> way up the chart to transcription, which is not true. So we need
>> to sort out this display so it accurately represents the
>> relationships and their traversal.
>>
>> You would need to think about whether you want to include the
>> regulates relationships as well, because if a protein regulates a
>> process, it is not necessarily directly involved in that process.
>> You probably wouldn't want to include regulates relations for
>> function terms as a protein that regulates a function probably
>> would not have that function itself, e.g. if it regulates a
>> kinase, it may not be a kinase itself.
>>
>> In QuickGO you can choose which relations you want to include in
>> a GO slim in the Filter -> GO Identifier menu (if you want
>> further help on this just let me know).
>>
>> I hope this explains it a little better? I am not brilliant with
>> has_part so if you have more questions, I could direct them to
>> one of the ontology editors who should know more than me!
>>
>> Best wishes,
>> Rachael.
>>
>>
>> On 03/02/2011 17:06, Heather Wick wrote:
>>> Hi Rachael,
>>> DFLAT is currently working on a gene set collection similar to
>>> what the Broad did in 2008 with its C5 collection, and as part
>>> of that we're trying to sort through all the parent-child
>>> relationships in GO to map gene sets of child terms to their
>>> parents. As far as I can tell, "is_a," "part_of," and
>>> "regulates" (including negatively_ and positively) describe
>>> parent-child relationships, but I'm a bit confused about the
>>> term "has_part." On this page
>>> http://www.geneontology.org/GO.ontology-ext.relations.shtml#haspart
>>> it says "A /necessarily has part/ B. If A exists, B will always
>>> exist; however, if B exists, we cannot say for certain that A
>>> exists." This suggests that if A has_part B, then B is a parent
>>> of A. Is that correct? Or is "has_part" not really considered to
>>> describe a parent-child relationship? For example, I noticed
>>> that "Urea cycle" has_part "argininosuccinate synthase
>>> activity," but "argininosuccinate synthase activity" is listed
>>> as not having any children.
>>>
>>> Aside from "is_a," "part_of,", and "regulates," are there any
>>> other terms that describe a parent-child relationship?
>>> Thanks,
>>> ~ Heather
>>>
>>> --
>>> Heather Wick
>>> Research Coordinator
>>> Tufts University Computer Science Department
>>> hwick at cs.tufts.edu
>>
>>
>> --
>> GOA and IntAct Curator
>> European Bioinformatics Institute
>> Welcome Trust Genome Campus
>> Hinxton
>> Cambridge, CB10 1SD
>> UK
>>
>> Tel: 01223 492515
>> Fax: 01223 494468
>> Email:huntley at ebi.ac.uk
>> GOA:http://www.ebi.ac.uk/GOA
>> IntAct:http://www.ebi.ac.uk/intact
>>
>>
>>
>>
>> --
>> Heather Wick
>> Research Coordinator
>> Tufts University Computer Science Department
>> hwick at cs.tufts.edu
>
>
> --
> GOA and IntAct Curator
> European Bioinformatics Institute
> Welcome Trust Genome Campus
> Hinxton
> Cambridge, CB10 1SD
> UK
>
> Tel: 01223 492515
> Fax: 01223 494468
> Email:huntley at ebi.ac.uk
> GOA:http://www.ebi.ac.uk/GOA
> IntAct:http://www.ebi.ac.uk/intact
>
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
--
Dr Rebecca Foulger
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492523
f: +44 1223 494468
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From hwick at cs.tufts.edu Thu Feb 10 10:03:27 2011
From: hwick at cs.tufts.edu (Heather Wick)
Date: Thu, 10 Feb 2011 13:03:27 -0500
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To: <4D53F54F.1080701@ebi.ac.uk>
References:
<4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk> <4D53F54F.1080701@ebi.ac.uk>
Message-ID:
Hi Rebecca,
Thanks for your help. I think if I explain a little more about what we're
doing it might help you guide us. We're not actually creating a GOslim, but
trying to make gene sets that we can upload into GSEA, based on the C5
collection that the Broad did in 2008. We are writing a program that does
this with the annotations downloaded from GO and using the OBO file to
create the GO tree. It's my understanding that when a curator annotates a
gene with a GO term, that gene is also annotated with all the parents,
grandparents, etc of the initial GO term. In making our gene sets, we were
told by the Broad that we should mimic this, but we are not sure how GO does
this since it's ambiguous what relationship terms denote true parent-child
relationships that dictate when a gene is 'exploded' through all the parent
terms. Specifically, we are not sure how to deal with 'regulates' which
seems to cross ontologies (and so does part_of?) in ways that gene sets
might not be carried through, as Rachael pointed out with her regulation of
kinase example.
So in light of that, my questions are these:
Is it appropriate to 'explode' gene sets up through parent annotations (or
just keep them annotated to the term the original curator gave them) when
making gene sets for GSEA? Would it be valid not to 'explode' the terms?
If we should carry up the gene sets, how does the GO do this? What
relationship terms determine this, especially in the case of 'regulates'
which crosses ontologies?
Is there any way of making this distinction for a term like 'regulates' from
information in the OBO file?
Again, thanks for your help!
~ Heather
On Thu, Feb 10, 2011 at 9:25 AM, Rebecca Foulger wrote:
>
> Dear Heather,f
>
> You probably don't want to follow has_part relationships for a slim,
> because they point from less specific to more specific (i.e. the opposite
> way to 'is_a' and 'part_of' relationships).
>
> For 'regulates' relationships, you should bear in mind that the parent is
> not necessarily more general than the child (unlike is_a and part_of). Like
> you say, you may want to include 'regulation of x process' but not
> 'regulation of y function' in your slims. For example, if you want to find
> kinases in your GOslim, you will not want to include gene products that
> regulate kinases but do not necessarily have kinase activity themselves.
> Whereas, if you want to find gene products involved in the cell cycle, it
> may also be useful to include gene products that regulate the cell cycle.
> There is extended documentation on the relations and reasoning on them at
> http://www.geneontology.org/GO.ontology-ext.relations.shtml.
>
> Since all 'regulation of x process' and 'regulation of y function' terms
> are process terms themselves, I do not know of a simple list separating the
> two types. Have you used the OBO-Edit tool before (listed at
> http://www.geneontology.org/GO.tools.shtml)? If so, you can download
> OBO-Edit, load the .obo file into OBO-Edit and do a search for GO terms that
> have 'regulation' in the term name, and have a molecular function parent to
> generate a list. You can also perform more complex queries on GO at:
> http://www.berkeleybop.org/goose.
>
> One of the developers may be able to help you write a more specific query.
>
> I hope that is of some help.
> With best wishes,
> Rebecca
>
>
>
>
> On 08/02/2011 11:52, Rachael Huntley wrote:
>
> Hi Heather,
>
> I am going to have to refer you to the ontology editors for these questions
> as they will undoubtedly give much better answers than I can.
>
> All: Heather would like to analyse a dataset but would like to know which
> relationships to include and which are considered parent-child. What are the
> implications of including/not including 'regulates' relationships in the
> analysis, especially for Function?
> Can you distinguish regulates terms that regulate processes from those that
> regulate function?
> Full story below.
>
> Thanks for your help.
>
> Rachael.
>
> On 07/02/2011 20:02, Heather Wick wrote:
>
> Hi Rachael,
>
> Thanks for the clarification on has_part, that helps a lot.
>
> Your point about regulation terms is something we had not yet considered
> and I'm glad you brought it up. I was under the impression that the process,
> function, and component ontologies were separate and that there were no
> relationships between them; so that all "regulation of" terms were
> biological process terms and had biological process parentage, even if they
> regulated an activity. But I see now that the "regulates" relationship can
> bridge the ontologies (thanks in part to the new color coded Graph View
> display in AmiGO). Is there any way to distinguish whether a term regulates
> something in its own ontology vs. a different ontology if we did want to
> keep the biological process regulation terms but not molecular function
> regulation terms? I've been trying to understand how we could determine that
> based on the information in this file, since this is the file we are writing
> our program around:
> http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
>
> Another point of confusion is that I can't find any explanations on what
> the terms "relationship:" and "intersection_of:" mean in this file, even in
> the informational sections on relationships (http://www.obofoundry.org/ro/,
> http://www.geneontology.org/GO.ontology.relations.shtml). Do they indicate
> a parent-child relationship? For that matter, are there any other terms
> besides "is_a" and "part_of" that describe "true" parent-child
> relationships?
>
> Just so I understand you correctly, are you saying that GO does not
> consider a term like "regulation of angiogenesis" to be a child of
> "angiogenesis?" I thought that these kinds of terms were considered to have
> a parent-child relationship and that the genes annotated to "regulation of
> angiogenesis" would also be annotated to "angiogenesis" and up through the
> tree automatically by GO. For what relationships does GO carry the
> annotation up?
>
>
> Thank you for all of your help!
> ~ Heather
>
> On Fri, Feb 4, 2011 at 5:17 AM, Rachael Huntley wrote:
>
>> Hi Heather,
>>
>> Yes, the has_part relationship is getting many people confused! It is not
>> a true parent-child relationship so I think you can ignore it for your
>> purposes.
>>
>> It is kind of a reverse relationship, so if you look at
>> http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004055#term=ancchart you see
>> that 'urea cycle' has_part 'arginosuccinate synthase activity' (the arrow
>> between the terms is going in the opposite direction), which means the urea
>> cycle always involves arginosuccinate synthase activity, but if a protein
>> has arginosuccinate synthase activity it is not necessarily taking part in
>> the urea cycle.
>>
>> On top of this, we are aware that QuickGO has some display issues with the
>> has_part relationships, which are misleading. So in the example of protein
>> phosphatase 2A binding (
>> http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0051721#term=ancchart) it looks
>> like protein phosphatase 2A binding is related all the way up the chart to
>> transcription, which is not true. So we need to sort out this display so it
>> accurately represents the relationships and their traversal.
>>
>> You would need to think about whether you want to include the regulates
>> relationships as well, because if a protein regulates a process, it is not
>> necessarily directly involved in that process. You probably wouldn't want to
>> include regulates relations for function terms as a protein that regulates a
>> function probably would not have that function itself, e.g. if it regulates
>> a kinase, it may not be a kinase itself.
>>
>> In QuickGO you can choose which relations you want to include in a GO slim
>> in the Filter -> GO Identifier menu (if you want further help on this just
>> let me know).
>>
>> I hope this explains it a little better? I am not brilliant with has_part
>> so if you have more questions, I could direct them to one of the ontology
>> editors who should know more than me!
>>
>> Best wishes,
>> Rachael.
>>
>>
>> On 03/02/2011 17:06, Heather Wick wrote:
>>
>> Hi Rachael,
>> DFLAT is currently working on a gene set collection similar to what the
>> Broad did in 2008 with its C5 collection, and as part of that we're trying
>> to sort through all the parent-child relationships in GO to map gene sets of
>> child terms to their parents. As far as I can tell, "is_a," "part_of," and
>> "regulates" (including negatively_ and positively) describe parent-child
>> relationships, but I'm a bit confused about the term "has_part." On this
>> page http://www.geneontology.org/GO.ontology-ext.relations.shtml#haspartit says "A
>> *necessarily has part* B. If A exists, B will always exist; however, if B
>> exists, we cannot say for certain that A exists." This suggests that if A
>> has_part B, then B is a parent of A. Is that correct? Or is "has_part" not
>> really considered to describe a parent-child relationship? For example, I
>> noticed that "Urea cycle" has_part "argininosuccinate synthase activity,"
>> but "argininosuccinate synthase activity" is listed as not having any
>> children.
>>
>> Aside from "is_a," "part_of,", and "regulates," are there any other terms
>> that describe a parent-child relationship?
>> Thanks,
>> ~ Heather
>>
>> --
>> Heather Wick
>> Research Coordinator
>> Tufts University Computer Science Department
>> hwick at cs.tufts.edu
>>
>>
>>
>> --
>> GOA and IntAct Curator
>> European Bioinformatics Institute
>> Welcome Trust Genome Campus
>> Hinxton
>> Cambridge, CB10 1SD
>> UK
>>
>> Tel: 01223 492515
>> Fax: 01223 494468
>> Email: huntley at ebi.ac.uk
>> GOA: http://www.ebi.ac.uk/GOA
>> IntAct: http://www.ebi.ac.uk/intact
>>
>>
>
>
> --
> Heather Wick
> Research Coordinator
> Tufts University Computer Science Department
> hwick at cs.tufts.edu
>
>
>
> --
> GOA and IntAct Curator
> European Bioinformatics Institute
> Welcome Trust Genome Campus
> Hinxton
> Cambridge, CB10 1SD
> UK
>
> Tel: 01223 492515
> Fax: 01223 494468
> Email: huntley at ebi.ac.uk
> GOA: http://www.ebi.ac.uk/GOA
> IntAct: http://www.ebi.ac.uk/intact
>
>
> _______________________________________________
> Ontology-editors mailing listOntology-editors at geneontology.orghttp://fafner.stanford.edu/mailman/listinfo/ontology-editors
>
>
>
> --
> Dr Rebecca Foulger
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492523
> f: +44 1223 494468
>
>
--
Heather Wick
Research Coordinator
Tufts University Computer Science Department
hwick at cs.tufts.edu
-------------- next part --------------
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From aji at ebi.ac.uk Thu Feb 10 10:37:32 2011
From: aji at ebi.ac.uk (Amelia Ireland)
Date: Thu, 10 Feb 2011 10:37:32 -0800
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To:
References:
<4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk> <4D53F54F.1080701@ebi.ac.uk>
Message-ID:
Hello Heather,
[snip]
> So in light of that, my questions are these:
> Is it appropriate to 'explode' gene sets up through parent
> annotations (or
> just keep them annotated to the term the original curator gave them)
> when
> making gene sets for GSEA? Would it be valid not to 'explode' the
> terms?
> If we should carry up the gene sets, how does the GO do this? What
> relationship terms determine this, especially in the case of
> 'regulates'
> which crosses ontologies?
> Is there any way of making this distinction for a term like
> 'regulates' from
> information in the OBO file?
This is a tricky area and at present there is not very much
information available on the GO website about transferring annotations
across different relationships. However, there is some draft
documentation at the top of the page here:
http://geneontology.org/GO.draft-page.shtml
(ignore the section marked 'Annotations and other relationships'
onwards)
As you can see, the annotation relationship "means" something
different according to which ontology the term is in; annotations to
component terms correspond to 'gene product A localizes to component
X', and annotations to function and process terms denote 'gp A has
function in process Y/function Z'. When these relations combine with
the ontology relations, you get different results; for example, if gp
A localizes to component X, and X is part of component N, we can say
that gp A localizes to component N. However, if gp A has function in
process Y, and process Y regulates function M, we says that gp A is a
regulator of M. The full set of relation combinations is shown on the
documentation page mentioned above.
Although it is possible to calculate relationships between ontology
terms from the information in the ontology file, there is no
information in the file about the annotation relationships at present.
This will be added at some point in the future when they have been
fully documented; this is an area of active work and development.
I hope that information helps!
Amelia.
--
Amelia Ireland
GO Editorial Office
http://www.berkeleybop.org || http://www.ebi.ac.uk
Preventing Euthanasia Through Rescue: http://petrescueinc.org
From hwick at cs.tufts.edu Thu Feb 10 14:21:31 2011
From: hwick at cs.tufts.edu (Heather Wick)
Date: Thu, 10 Feb 2011 17:21:31 -0500
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To:
References:
<4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk> <4D53F54F.1080701@ebi.ac.uk>
Message-ID:
Thanks for the information.
Given that there isn't a lot of information about how the GO does this, we
are now wondering if it would be considered good practice to make the gene
sets *without* transferring the gene sets up through the tree -- do you have
an opinion about this? After all, does it make sense for us to try to
imitate what the GO is doing to 'explode' genes across relationship terms
when someone makes an annotation if we can't replicate it exactly? How does
the GO do it -- is it done manually or automatically? If automatically,
would it be possible for us to look at how it's being done?
I appreciate any input you all might have.
~ Heather
On Thu, Feb 10, 2011 at 1:37 PM, Amelia Ireland wrote:
> Hello Heather,
> [snip]
>
> So in light of that, my questions are these:
>> Is it appropriate to 'explode' gene sets up through parent annotations (or
>> just keep them annotated to the term the original curator gave them) when
>> making gene sets for GSEA? Would it be valid not to 'explode' the terms?
>> If we should carry up the gene sets, how does the GO do this? What
>> relationship terms determine this, especially in the case of 'regulates'
>> which crosses ontologies?
>> Is there any way of making this distinction for a term like 'regulates'
>> from
>> information in the OBO file?
>>
>
>
> This is a tricky area and at present there is not very much information
> available on the GO website about transferring annotations across different
> relationships. However, there is some draft documentation at the top of the
> page here:
>
> http://geneontology.org/GO.draft-page.shtml
>
> (ignore the section marked 'Annotations and other relationships' onwards)
>
> As you can see, the annotation relationship "means" something different
> according to which ontology the term is in; annotations to component terms
> correspond to 'gene product A localizes to component X', and annotations to
> function and process terms denote 'gp A has function in process Y/function
> Z'. When these relations combine with the ontology relations, you get
> different results; for example, if gp A localizes to component X, and X is
> part of component N, we can say that gp A localizes to component N. However,
> if gp A has function in process Y, and process Y regulates function M, we
> says that gp A is a regulator of M. The full set of relation combinations is
> shown on the documentation page mentioned above.
>
> Although it is possible to calculate relationships between ontology terms
> from the information in the ontology file, there is no information in the
> file about the annotation relationships at present. This will be added at
> some point in the future when they have been fully documented; this is an
> area of active work and development.
>
> I hope that information helps!
>
> Amelia.
>
> --
> Amelia Ireland
> GO Editorial Office
> http://www.berkeleybop.org || http://www.ebi.ac.uk
> Preventing Euthanasia Through Rescue: http://petrescueinc.org
>
>
>
>
--
Heather Wick
Research Coordinator
Tufts University Computer Science Department
hwick at cs.tufts.edu
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From admin at genome.stanford.edu Mon Feb 14 09:06:23 2011
From: admin at genome.stanford.edu (Administrator)
Date: Mon, 14 Feb 2011 09:06:23 -0800
Subject: [Ontology-editors] testing
Message-ID: <201102141706.p1EH6NEo028662@meatloaf.Stanford.EDU>
testing script command.
From aji at ebi.ac.uk Wed Feb 16 12:34:19 2011
From: aji at ebi.ac.uk (Amelia Ireland)
Date: Wed, 16 Feb 2011 12:34:19 -0800
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To:
References:
<4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk> <4D53F54F.1080701@ebi.ac.uk>
Message-ID: <6505C636-3B80-488E-816B-8C04735434DC@ebi.ac.uk>
On 10 Feb 2011, at 14:21, Heather Wick wrote:
> Thanks for the information.
> Given that there isn't a lot of information about how the GO does
> this, we
> are now wondering if it would be considered good practice to make
> the gene
> sets *without* transferring the gene sets up through the tree -- do
> you have
> an opinion about this?
It makes it a lot easier to share and compare results if you do have
annotations propagating through the tree, i.e. broader terms
'inheriting' the annotations from the more specific terms. This is
particularly true if areas of the ontology have undergone development
and new terms have been added, or you might have data from sources
with differing levels of annotation specificity.
> After all, does it make sense for us to try to
> imitate what the GO is doing to 'explode' genes across relationship
> terms
> when someone makes an annotation if we can't replicate it exactly?
> How does
> the GO do it -- is it done manually or automatically? If
> automatically,
> would it be possible for us to look at how it's being done?
> I appreciate any input you all might have.
The propagation of annotations is done automatically during the
generation of the GO database, using the rules that I mentioned in my
previous email. You can find the code in go-dev (hosted on
SourceForge; http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/)
in the go-perl and go-db-perl distributions.
I hope that helps!
Thanks,
Amelia Ireland.
--
Amelia Ireland
GO Editorial Office
http://www.berkeleybop.org || http://www.ebi.ac.uk
Preventing Euthanasia Through Rescue: http://petrescueinc.org
From hwick at cs.tufts.edu Wed Feb 16 13:46:14 2011
From: hwick at cs.tufts.edu (Heather Wick)
Date: Wed, 16 Feb 2011 16:46:14 -0500
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To: <6505C636-3B80-488E-816B-8C04735434DC@ebi.ac.uk>
References:
<4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk> <4D53F54F.1080701@ebi.ac.uk>
<6505C636-3B80-488E-816B-8C04735434DC@ebi.ac.uk>
Message-ID:
Thank you for the advice. Do you happen to know what files specifically to
look at in those folders for the mapping? There's quite a number of files
and the readme does not seem to be very specific. If not, we can sort
through it -- but I figured I'd ask. Again, thanks!
~ Heather
On Wed, Feb 16, 2011 at 3:34 PM, Amelia Ireland wrote:
>
> On 10 Feb 2011, at 14:21, Heather Wick wrote:
>
> Thanks for the information.
>> Given that there isn't a lot of information about how the GO does this, we
>> are now wondering if it would be considered good practice to make the gene
>> sets *without* transferring the gene sets up through the tree -- do you
>> have
>> an opinion about this?
>>
>
> It makes it a lot easier to share and compare results if you do have
> annotations propagating through the tree, i.e. broader terms 'inheriting'
> the annotations from the more specific terms. This is particularly true if
> areas of the ontology have undergone development and new terms have been
> added, or you might have data from sources with differing levels of
> annotation specificity.
>
>
> After all, does it make sense for us to try to
>> imitate what the GO is doing to 'explode' genes across relationship terms
>> when someone makes an annotation if we can't replicate it exactly? How
>> does
>> the GO do it -- is it done manually or automatically? If automatically,
>> would it be possible for us to look at how it's being done?
>> I appreciate any input you all might have.
>>
>
> The propagation of annotations is done automatically during the generation
> of the GO database, using the rules that I mentioned in my previous email.
> You can find the code in go-dev (hosted on SourceForge;
> http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/) in
> the go-perl and go-db-perl distributions.
>
> I hope that helps!
>
> Thanks,
> Amelia Ireland.
>
>
> --
> Amelia Ireland
> GO Editorial Office
> http://www.berkeleybop.org || http://www.ebi.ac.uk
> Preventing Euthanasia Through Rescue: http://petrescueinc.org
>
>
>
>
--
Heather Wick
Research Coordinator
Tufts University Computer Science Department
hwick at cs.tufts.edu
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From aji at ebi.ac.uk Wed Feb 16 13:56:46 2011
From: aji at ebi.ac.uk (Amelia Ireland)
Date: Wed, 16 Feb 2011 13:56:46 -0800
Subject: [Ontology-editors] "has_part" and parent-child relationships
In-Reply-To:
References:
<4D4BD21C.4070003@ebi.ac.uk>
<4D512E9B.2060208@ebi.ac.uk> <4D53F54F.1080701@ebi.ac.uk>
<6505C636-3B80-488E-816B-8C04735434DC@ebi.ac.uk>
Message-ID: <5E5BDDAE-798C-4875-B0D2-BCAB806CFACA@ebi.ac.uk>
On 16 Feb 2011, at 13:46, Heather Wick wrote:
> Thank you for the advice. Do you happen to know what files
> specifically to
> look at in those folders for the mapping? There's quite a number of
> files
> and the readme does not seem to be very specific. If not, we can sort
> through it -- but I figured I'd ask. Again, thanks!
I've asked the database team and the guy who wrote the code for
clarification as I don't use this code so I'm not all that familiar
with it. By the looks of things, you will need to look in go-db-perl
and trace the 'fill_count_table' sub as that appears to be populating
the GP counts in the database. I will let you know if I hear any
different from the other developers.
Good luck!
Amelia.
--
Amelia Ireland
GO Editorial Office
http://www.berkeleybop.org || http://www.ebi.ac.uk
Preventing Euthanasia Through Rescue: http://petrescueinc.org
From rfoulger at ebi.ac.uk Fri Feb 25 08:28:15 2011
From: rfoulger at ebi.ac.uk (Rebecca Foulger)
Date: Fri, 25 Feb 2011 16:28:15 +0000
Subject: [Ontology-editors] cell-type specific, and protein-specific GO terms
Message-ID: <4D67D89F.9040507@ebi.ac.uk>
Dear ontology editors,
Please can I get feedback/advice on adding in cell-type-specific process
terms & protein-specific function terms.
In the absence of most curators being able to use column 16, there's an
influx of SF requests from Evelyn for cell migration terms for specific
cell types, and binding terms for specific cytokines.
We already have many examples of these kind of terms in GO, but I'm
unclear whether these existing terms will be obsoleted when column 16 is
up and running, and whether we should keep adding them in the meantime?
Thank you,
Becky
https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=440764
--
Dr Rebecca Foulger
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492523
f: +44 1223 494468
From cjmungall at lbl.gov Fri Feb 25 09:27:46 2011
From: cjmungall at lbl.gov (Chris Mungall)
Date: Fri, 25 Feb 2011 12:27:46 -0500
Subject: [Ontology-editors] cell-type specific,
and protein-specific GO terms
In-Reply-To: <4D67D89F.9040507@ebi.ac.uk>
References: <4D67D89F.9040507@ebi.ac.uk>
Message-ID: <53829AE6-E2AD-4A8F-AF4E-96BE355E853B@lbl.gov>
We can make TG templates once the bp_xp_cl logical definitions are incorporated. whether we do it this way or with c16 or the old manual way we have to figure out and document the templates.
E.g.
>GO:0072683 T cell extravasation
>> GO new: CD8-positive alpha-beta T cell extravasation
>>>GO new: positive regulation of CD8-positive alpha-betaT cell extravasation
>>>GO new: negative regulation of CD8-positive alpha-betaT cell extravasation
>>>>GO new: CD8-positive, alpha-beta cytotoxic T cell extravasation
>>>>>GO new: positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation
>>>>>GO new: negative regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation
is migration just movement between tissues?
is extravision just movement where the initial location is the inside of blood vessels?
On Feb 25, 2011, at 11:28 AM, Rebecca Foulger wrote:
>
> Dear ontology editors,
>
> Please can I get feedback/advice on adding in cell-type-specific process terms & protein-specific function terms.
>
> In the absence of most curators being able to use column 16, there's an influx of SF requests from Evelyn for cell migration terms for specific cell types, and binding terms for specific cytokines.
>
> We already have many examples of these kind of terms in GO, but I'm unclear whether these existing terms will be obsoleted when column 16 is up and running, and whether we should keep adding them in the meantime?
>
> Thank you,
> Becky
>
> https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=440764
>
>
>
> --
> Dr Rebecca Foulger
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492523
> f: +44 1223 494468
>
> _______________________________________________
> Ontology-editors mailing list
> Ontology-editors at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/ontology-editors
From cjmungall at lbl.gov Mon Feb 28 08:39:36 2011
From: cjmungall at lbl.gov (Chris Mungall)
Date: Mon, 28 Feb 2011 08:39:36 -0800
Subject: [Ontology-editors] Term Genie feature requests & email notification
Message-ID: <1D833212-6CC9-4E57-82C0-2371F83442F2@lbl.gov>
We don't really have a TG request tracker set up right now. Generally the protocol is: if it's easy I'll add it, if not I'll punt. I think a few people have requested some kind of email/notification feature. This is a little fiddly to set up with TG right now.
When Heiko starts in a few months I will have him work in parallel on a TG2 that should be more extensible and feature-ful. In the meantime I could set up a project on googlecode with a tracker so you can provide feature requests there.
We could have a system (separate from TG) that provides notification on ontology changes, such that people can subscribe to changes (e.g. terms with a particular definition dbxref)